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Hi Nicolas,<br>
<br>
There is not a command to shift or position an oblique volume
slice. I agree that would be useful and will put a feature request
in our database for it.<br>
<br>
Here's a way to do what you want. Use the subregion selection
green outline to crop to a rotated box. Make the box have a
thickness that covers your structure of interest. This creates a
new volume shown in the volume dialog and you can use the Planes
panel to flip through planes of that rotated volume separated by
precisely the grid spacing. The grid spacing can be specified using
the entry field at the end of the "Rotate selection box" line in the
subregion panel. It defaults to match the original data set grid
spacing. To control the width and height of the rotated volume you
can use the Region Bounds panel of the volume dialog to specify
exactly how many voxels to use along each axis for display of the
rotated volume.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Axis vs map rotation<br>
From: Nicolas Coudray <br>
To: Tom Goddard <br>
Date: 12/8/11 6:08 AM<br>
<blockquote cite="mid:20111208140831.69d12d0f@nysbc.org" type="cite">
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Hello Tom,<br>
<br>
Thanks for the answer... <br>
It is a nice alternative. Although, it's kind of more difficult to
manually translate a precise amount of nm. Is there a way, like
with the "plane" option, to control precisely the width and the
translation of the subregion box? Maybe through a command line,
but I have found it... <br>
<br>
Thanks again for the help,<br>
Nicolas<br>
<br>
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*<br>
<blockquote style="padding-left: 5px; margin-left: 5px;
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<hr><b>From:</b> Tom Goddard<br>
<b>To:</b> Nicolas Coudray<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
<b>Sent:</b> Wed, 07 Dec 2011 19:00:01 -0500<br>
<b>Subject:</b> Re: [Chimera-users] Axis vs map rotation<br>
<br>
Hi Nicolas,<br>
<br>
To show an oblique slice of a map you can use the volume
dialog "subregion selection" panel. The "planes" panel can only
display slices perpendicular to the volume axes as you found.
There's a video showing how to show the oblique slice on the
Chimera video tutorial web page<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.cgl.ucsf.edu/chimera/videodoc/slice/index.html">http://www.cgl.ucsf.edu/chimera/videodoc/slice/index.html</a><br>
<br>
The Chimera volume guide has a text description of the
procedure.<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#resample">http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#resample</a><br>
<br>
Tom<br>
<br>
<br>
<blockquote type="cite"> Hi,<br>
<br>
I'm using the "Feature >> Plane" options of the "Volume
viewer tool" to show contour lines in planes of density maps.
For the plane, there are 3 options: "X-axis", "Y-axis", and
"Z-axis". The plane I'm interested in is none of those. I try
to rotate the maps, but the X, Y and Z axis are also
rotating... Do you know if there's a way to rotate the "axis"
and the "map" independently, please?<br>
<br>
Thanks in advance,<br>
Nicolas<br>
<br>
</blockquote>
<br>
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